adaptBackground: Adapt background for a simulated 4C-seq sample
In walter-ca/Basic4CSim: Basic4CSim: Simulation of 4C-seq data

Description Usage Arguments Value Author(s) Examples

This helper function adapts the already simulated background for a simulated 4C-seq sample. The read count for blind fragments is reduced by a given factor (default: 0.2), coverage around the viewpoint is reduced to a certain rate (optional), and the general background read count per fragment is reduced with higher distance from the experiment's viewpoint (optional).

1 2	adaptBackground(simTable, vpStart, vpRegionDist = 1000000, vpCovRate = 0.95, blindFactor = 0.2, useNormDist = FALSE, minVal = 1000)

`simTable`	virtual simulation fragment library, with background
`vpStart`	position of the experiment's viewpoint
`vpRegionDist`	length of adapted region
`vpCovRate`	coverage rate of background around viewpoint (default: 0.95)
`blindFactor`	factor for blind fragment read count (default: 0.2)
`useNormDist`	if TRUE, fragments with higher distance from viewpoint will receive fewer reads (to blend transition from near-cis to cis)
`minVal`	minimum read count of fragments to be considered for near-cis adaption

Data frame with adapted simulated background reads

Carolin Walter

    if(interactive()) {
        simTableFile <- system.file("extdata", "simTable_noise.csv", 
            package="Basic4CSim")
        simTable = read.csv(simTableFile, sep = "\t", header = TRUE)
        vpStart = 69999869
        set.seed(42)
        simTable = adaptBackground(simTable, vpStart, useNormDist = TRUE,
            vpRegionDist = 150000)
        head(simTable)
    }